Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018761.1 Corchorus olitorius cultivar O-4 contig18794, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2260
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26


Found at i:524 original size:28 final size:29

Alignment explanation


    Indices: 465--614  Score: 232
    Period size: 29  Copynumber: 5.2  Consensus size: 29

        455 GAAGAGACAG

                *     *       *          
        465 AAATACCCCTAGATGTGCGAAAATGACCA
          1 AAATGCCCCTGGATGTGCAAAAATGACCA

                                         
        494 AAATGCCCCTGGATGTGC-AAAATGACCA
          1 AAATGCCCCTGGATGTGCAAAAATGACCA

                                         
        522 AAATGCCCCTGGATGTGCAAAAATGACCA
          1 AAATGCCCCTGGATGTGCAAAAATGACCA

                   *                     
        551 AAATGCCACTGGATGTGC-AAAATGACCA
          1 AAATGCCCCTGGATGTGCAAAAATGACCA

            *      *                     
        579 GAATGCCACTGGATGTGCAAAAATGACCA
          1 AAATGCCCCTGGATGTGCAAAAATGACCA

                   
        608 AAATGCC
          1 AAATGCC

        615 ACTGTATGAG


Statistics
Matches: 114,  Mismatches: 5, Indels: 4
        0.93            0.04        0.03

Matches are distributed among these distances:
  28   55  0.48
  29   59  0.52

ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17


Consensus pattern (29 bp):   
AAATGCCCCTGGATGTGCAAAAATGACCA

Found at i:563 original size:57 final size:57

Alignment explanation


    Indices: 465--618  Score: 254
    Period size: 57  Copynumber: 2.7  Consensus size: 57

        455 GAAGAGACAG

                *     *       *                 *                    
        465 AAATACCCCTAGATGTGCGAAAATGACCAAAATGCCCCTGGATGTGCAAAATGACCA
          1 AAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATGTGCAAAATGACCA

                                                                     
        522 AAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATGTGCAAAATGACCA
          1 AAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATGTGCAAAATGACCA

            *      *                                
        579 GAATGCCACTGGATGTGCAAAAATGACCAAAATGCCACTG
          1 AAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCACTG

        619 TATGAGTGAC


Statistics
Matches: 91,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  57   91  1.00

ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18


Consensus pattern (57 bp):   
AAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCACTGGATGTGCAAAATGACCA

Found at i:615 original size:29 final size:28

Alignment explanation


    Indices: 476--618  Score: 232
    Period size: 28  Copynumber: 5.0  Consensus size: 28

        466 AATACCCCTA

                                     *   
        476 GATGTGCGAAAATGACCAAAATGCCCCTG
          1 GATGTGC-AAAATGACCAAAATGCCACTG

                                    *   
        505 GATGTGCAAAATGACCAAAATGCCCCTG
          1 GATGTGCAAAATGACCAAAATGCCACTG

                                         
        533 GATGTGCAAAAATGACCAAAATGCCACTG
          1 GATGTGC-AAAATGACCAAAATGCCACTG

                             *          
        562 GATGTGCAAAATGACCAGAATGCCACTG
          1 GATGTGCAAAATGACCAAAATGCCACTG

                                         
        590 GATGTGCAAAAATGACCAAAATGCCACTG
          1 GATGTGC-AAAATGACCAAAATGCCACTG

        619 TATGAGTGAC


Statistics
Matches: 109,  Mismatches: 3, Indels: 4
        0.94            0.03        0.03

Matches are distributed among these distances:
  28   55  0.50
  29   54  0.50

ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17


Consensus pattern (28 bp):   
GATGTGCAAAATGACCAAAATGCCACTG

Found at i:1306 original size:18 final size:18

Alignment explanation


    Indices: 1263--1306  Score: 54
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1253 ATATTTAATT

                              
       1263 CTAATTTTAATATTATTA
          1 CTAATTTTAATATTATTA

            *  *               
       1281 TTATTTTTAAT-TTATATA
          1 CTAATTTTAATATTAT-TA

                    
       1299 CTAATTTT
          1 CTAATTTT

       1307 TCTTGGATTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 2
        0.78            0.15        0.07

Matches are distributed among these distances:
  17    4  0.19
  18   17  0.81

ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61


Consensus pattern (18 bp):   
CTAATTTTAATATTATTA
Done.